Primer Design

Utilities for creating primers for site directed mutagenesis

Colab

Site Directed Mutagenesis Primer Design

primer_design.sdm.design_primer:

Design a forward primer for SDM.
    
Args:
    dna_seq (str): DNA sequence to mutate.
    wt_resn (str): Wildtype residue.
    mut_resi (int): Residue position to mutate.
    mut_resn (str): Mutant residue.
    max_pad (int): Maximum number of nucleotides to pad the codon with. Default is 20.
    min_pad (int): Minimum number of nucleotides to pad the codon with. Default is 10.
    primer_conc (float): Primer concentration in nM. Default is 500.
    GC_3prime (bool): Filter forward primers so that 3' is G or C . Default is True.
    GC_5prime (bool): Filter forward primers so that 5' is G or C . Default is False.
    TM_target (float): Target melting temperature. Default is 70.
    polymerase (str): Polymerase used for PCR. Default is 'Phusion'.
    verbose (bool): Print information about primer design. Default is False.
    GC_max (float): Maximum GC content. Default is 0.8.
    TM_diff_max (float): Optional: Maximum allowable difference in melting temperature between forward and reverse primers. Default is None.
    show_gap (bool): Add gap to primer to indicate where codon is. Default is True.

Returns:
    primer_df (pd.DataFrame): Dataframe containing all possible primers.
        

Additional Utilities:

Codon Table:

primer_design.codon_table

• primer_design.codon_table['CODON'] -> 'AMINO ACID'

primer_design.codon_freq

• primer_design.codon_freq['CODON'] -> FREQ

primer_design.highest_freq_codon(target_resn):

• Get the highest frequency codon for a given amino acid
• Args: target_resn (str): target amino acid
• Returns: codon (str)
• Example: highest_freq_codon('A') -> 'GCG'

GC Content

primer_design.gc_content

• primer_design.gc_content('GCAA') -> 0.5

TM Calculator

primer_design.calculate_tm_nearest_neighbor(primer_sequence, primer_conc (in nM), polymerase) SUPPORTED_POLYMERASES:

• Phusion
• Phusion Hot Start Flex
• Q5
• Q5 Hot Start
• Q5 Blood Direct
• Q5U Hot Start
• OneTaq
• OneTaq Hot Start
• Hot Start Taq
• Taq
• LongAmp Taq
• LongAmp Hot Start Taq
• Hemo KlenTaq
• EpiMark Hot Start